Variant report

Variant	rs1551446
Chromosome Location	chr4:173423366-173423367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10006633	1.00[MEX][hapmap]
rs11132947	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11939125	0.89[EUR][1000 genomes]
rs13103453	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13107068	0.89[EUR][1000 genomes]
rs13113495	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13118772	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs13122643	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13140679	0.84[CEU][hapmap]
rs13142236	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs13146091	0.84[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap]
rs13146384	0.95[CEU][hapmap];0.90[GIH][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs13150574	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1455122	0.95[CEU][hapmap]
rs1455123	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap]
rs17233636	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2085207	0.95[CEU][hapmap]
rs2124204	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2332516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs337981	0.90[CEU][hapmap]
rs337994	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs338005	1.00[CEU][hapmap]
rs338047	0.87[ASW][hapmap];0.95[CEU][hapmap];0.90[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap]
rs338048	1.00[CEU][hapmap]
rs338049	0.81[CEU][hapmap]
rs338052	1.00[CEU][hapmap]
rs338054	1.00[CEU][hapmap]
rs338056	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs538624	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6812783	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7656178	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap]
rs7659363	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7669065	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs7686403	1.00[CEU][hapmap]
rs7686995	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs7694525	1.00[CEU][hapmap];0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031592	chr4:173112542-173662991	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv537359	chr4:173112542-173662991	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534293	chr4:173121379-173606082	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1031327	chr4:173306405-173465248	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv508333	chr4:173369686-173447675	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv4607	chr4:173406293-173457588	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv870205	chr4:173409062-173436383	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv596210	chr4:173409387-173431679	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1026882	chr4:173410691-173441120	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
11	nsv1016549	chr4:173411663-173441120	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
12	nsv1023134	chr4:173412218-173455427	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1021404	chr4:173413885-173458833	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	nsv263	chr4:173418319-173438806	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
15	esv1838024	chr4:173422260-173441120	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a
16	esv1813301	chr4:173422510-173441120	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a
17	esv3464632	chr4:173423077-173435475	Enhancers	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1551446	GALNTL6	cis	cerebellum	SCAN
rs1551446	WDR17	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
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